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Materials representation and transfer learning for multi-property prediction

Authors: Shufeng Kong 1, Dan Guevarra 2, Carla P. Gomes 1, and John M. Gregoire 2

  1. Department of Computer Science, Cornell University, Ithaca, NY, USA
  2. Division of Engineering and Applied Science, California Institure of Technology, Pasadena, CA, USA

We introduce the Hierarchical Correlation Learning for Multi-property Prediction framework (H-CLMP, pronounced H-CLAMP) that seamlessly integrates (i) prediction using only a material’s composition, (ii) learning and exploitation of correlations among target properties in multi-target regression, and (iii) leveraging training data from tangential domains via generative transfer learning. The model is demonstrated for prediction of spectral optical absorption of complex metal oxides spanning 69 3-cation metal oxide composition spaces. H-CLMP accurately predicts non-linear composition-property relationships in composition spaces for which no training data is available, which broadens the purview of machine learning to the discovery of materials with exceptional properties. This achievement results from the principled integration of latent embedding learning, property correlation learning, generative transfer learning, and attention models. The best performance is obtained using H-CLMP with Transfer learning (H-CLMP(T)) wherein a generative adversarial network is trained on computational density of states data and deployed in the target domain to augment prediction of optical absorption from composition. H-CLMP(T) aggregates multiple knowledge sources with a framework that is well-suited for multi-target regression across the physical sciences.

This is a Pytorch implementation of the H-CLMP model.

The paper is avaiable here https://arxiv.org/abs/2106.02225

Datasets

The spectral optical absorption dataset and a discription of the dataset can be found in https://data.caltech.edu/records/1878. To run our software, we need addtional DOS dataset from the material project https://materialsproject.org/. Therefore, we provide a colloection of all the necessary datasets to run our software in this link https://www.cs.cornell.edu/gomes/udiscoverit/?tag=materials. Please download the data.zip file and place in the main folder and unzip them.

Enviroments

This software relies a number of packages:

Pytorch 1.7.1

Numpy 1.20.1

torch_scatter 2.0.6

json 2.0.9

tqdm 4.42.1

Usages

1 and 2 can be ignored if you have downloaded our dataset from our provided Google drive lnk, we have done these for you.

1). Pretrain a WGAN for transfer learning.

Change your current directory to the main folder and run:

python WGAN_for_DOS/train_GAN.py

To test the quality of the generated DOS:

python WGAN_for_DOS/test_GAN.py

2). Preprocess datasets

2.1 Copy the 'WGAN.py' and the pretrained WGAN model 'generator_MP2020.pt' to the 'uvis_dataset_no_redundancy' folder.

Change your current directory to the 'data/uvis_dataset_no_redundancy' folder and run:

python process.py

This will generate train/test indices (validation set is a subset of the train set, see the 'data/uvis_dataset_no_redundancy/idx' folder) and a dictionary X. Each entry of X is a data entry, which is also a dictionary including keys:

'fom': the material properties' label, representing the 10 dimension observation energy.

'composition_nonzero': the fraction of existing elements in the compound.

'composition_nonzero_idx': the corresponding indices of the existing elements in the array ['Ag', 'Ba', 'Bi', 'Ca', 'Ce', 'Co', 'Cr', 'Cu', 'Er', 'Eu', 'Fe', 'Ga', 'Gd', 'Hf', 'In', 'K', 'La', 'Mg', 'Mn', 'Mo', 'Nb', 'Nd', 'Ni', 'P', 'Pb', 'Pd', 'Pr', 'Rb', 'Sc', 'Sm', 'Sn', 'Sr', 'Tb', 'Ti', 'V', 'W', 'Yb', 'Zn', 'Zr'].

'nonzero_element_name': the names of the existing elements in the compound.

'gen_dos_fea': the generated DOS feature for the compound by using the pretrained WGAN model.

'composition': the traction of all considered elements (['Ag', 'Ba', 'Bi', 'Ca', 'Ce', 'Co', 'Cr', 'Cu', 'Er', 'Eu', 'Fe', 'Ga', 'Gd', 'Hf', 'In', 'K', 'La', 'Mg', 'Mn', 'Mo', 'Nb', 'Nd', 'Ni', 'P', 'Pb', 'Pd', 'Pr', 'Rb', 'Sc', 'Sm', 'Sn', 'Sr', 'Tb', 'Ti', 'V', 'W', 'Yb', 'Zn', 'Zr']) in the compound

2.2 Copy the 'WGAN.py' and the pretrained WGAN model 'generator_MP2020.pt' to the 'data/uvis_dataset_no_gt' folder.

Change your current directory to the 'data/uvis_dataset_no_gt' folder and run:

python process.py

3). Example of training and testing the HCLMP model.

3.1 Change your current directory to the main folder and run:

python jobs.py

This can be used to train/test the random split setting or the 69 ternary systems.

3.2 You can also run jobs in parallel (this needs to revise the script base on your GPU numbers and memory. Read the script for details):

bash jobs_parallel.sh

This can be used to train/test the 69 ternary systems in parallel.

3.3 To train a model on all labelled data and test the model on new data without ground-truth:

python job_no_gt.py

This is for the experiment of "deployment for materials discovery" section in the paper.

Copyright

The graph encoder we adopted takes the element embedding and element fraction as input and produces a latent embedding. This piece of codes is modified from Goodall and Lee, Predicting materials properties without crystal structure: deep representation learning from stoichiometry, Nature communication, 2020. Copyright of the graph encoder belongs to the authors. Please see the Github Link: https://github.com/CompRhys/roost for details.